Define where the pipeline should find input data and save output data.

Path to comma-separated file containing information about the samples in the experiment.

required
type: string
pattern: ^\S+\.csv$

Path to comma-separated file containing the sample names for the desired paired comparisons.

type: string

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

required
type: string

Email address for completion summary.

type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

type: string

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string

Path to FASTA genome file.

type: string
pattern: ^\S+\.fn?a(sta)?(\.gz)?$

Do not load the iGenomes reference config.

type: boolean
default: true

The base path to the igenomes reference files

hidden
type: string
default: s3://ngi-igenomes/igenomes

Specify aligner to be used to map reads to reference genome.

type: string

Specify the program to use for read trimming

type: string

Path to directory or tar.gz archive for pre-built BWA index.

type: string

If generated by the pipeline save the aligner index (e.g. BWA) in the results directory.

type: boolean

Path to directory or tar.gz archive for pre-built bowtie2 index.

type: string

If generated by the pipeline save the BWA index in the results directory.

type: boolean

A BED or GTF file containing regions that should be excluded from all analyses.

type: string

Parameters used to describe centralised config profiles. These should not be edited.

Git commit id for Institutional configs.

hidden
type: string
default: master

Base directory for Institutional configs.

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/configs/master

Institutional config name.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

Less common options for the pipeline, typically set in a config file.

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

Email address for completion summary, only when pipeline fails.

hidden
type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Send plain-text email instead of HTML.

hidden
type: boolean

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string

Custom config file to supply to MultiQC.

hidden
type: string

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

hidden
type: string

Custom MultiQC yaml file containing HTML including a methods description.

type: string

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Base URL or local path to location of pipeline test dataset files

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/test-datasets/

Specify after which step the pipeline should stop.

hidden
type: string
hidden
type: boolean

Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.

hidden
type: string

Defines how much the reads should be extended

type: integer

bw_resolution (expressed in base pairs) for genome coverage calculation (default 1).

type: integer
default: 1

Method selecte to perform the normalizazion

type: string

Estimated genome size to performing the normalization

type: integer

A list of space-delimited chromosome names containing those chromosomes that should be excluded for computing the normalization

type: string

If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate\u2019s position also has to coincide to ignore a read

type: boolean

-L options filter the alignments that will be included in the output to only those alignments that match certain criteria.

type: string

kip alignments with MAPQ smaller than ‘value’ (1 default).

type: integer
default: 1

If set filter reads based on specific flags. Flags represent various properties of a read, such as whether it’s mapped, paired, or properly aligned (default 1540)

type: integer
default: 1540

Region of the genome to limit the operation to - this is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example –region chr10 or –region chr10:456700:891000.

type: string

The number of bins that are sampled from the genome, for which the overlapping number of reads is computed. (Default: 500000)

type: integer
default: 500000

Deeptools multiBamSummary bam bin size (Default 50000).

type: integer

Deeptools Correlation Plot statistical calculation method

type: string

Fragment size parameter for single-end data. When set to a positive value, it enables the —extendReads option in DeepTools, extending reads to the specified length. This parameter is only used for single-end data processing and does not affect paired-end data analysis.

hidden
type: integer
default: 100

Optionally provide chromosome sizes file as input

type: string

Optionally provide FASTA index (.fai) file as input

type: string

Path to GTF annotation file.

type: string

Path to BED file containing gene intervals. This will be created from the GTF file if not specified.

type: string